Vinay Nandicoori - Academia.edu (original) (raw)

Papers by Vinay Nandicoori

Biochemical Journal, 2021

N-acetyl glucosamine-1-phosphate uridyltransferase (GlmU) is a bifunctional enzyme involved in th... more N-acetyl glucosamine-1-phosphate uridyltransferase (GlmU) is a bifunctional enzyme involved in the biosynthesis of Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is a critical precursor for the synthesis of peptidoglycan and other cell wall components. The absence of a homolog in eukaryotes makes GlmU an attractive target for therapeutic intervention. Mycobacterium tuberculosis GlmU (GlmUMt) has features, such as a C-terminal extension, that are not present in GlmUorthologs from other bacteria. Here, we set out to determine the uniqueness of GlmUMt by performing in vivo complementation experiments using RvΔglmU mutant. We found that any deletion of the carboxy-terminal extension region of GlmUMt abolishes its ability to complement the function of GlmUMt. Results show orthologs of GlmU, including its closest ortholog, from Mycobacterium smegmatis, cannot complement the function of GlmUMt. Furthermore, the co-expression of GlmUMt domain deletion mutants with either a...

The Journal of Infectious Diseases, 2021

Attenuated intracellular survival of Mycobacterium tuberculosis (Mtb) secretory gene mutants exem... more Attenuated intracellular survival of Mycobacterium tuberculosis (Mtb) secretory gene mutants exemplifies their role as virulence factors. Mtb peptidyl prolyl isomerase A (PPiA) assists in protein folding through cis/trans isomerization of prolyl bonds. Here, we show that PPiA abets Mtb survival and aids in disease progression by exploiting host-associated factors. While the deletion of PPiA has no discernable effect on bacillary survival in a murine infection model, it compromises the formation of granuloma-like lesions and promotes host cell death through ferroptosis. Overexpression of PPiA enhances the bacillary load and exacerbates pathology in mice lungs. Importantly, PPiA interacts with the integrin α5β1 receptor through a conserved surface-exposed RGD motif. The secretion of PPiA as well as interaction with integrin contributes to disease progression by upregulating multiple host matrix metalloproteinases. Collectively, we identified a novel nonchaperone role of PPiA that is c...

Antimicrobial Agents and Chemotherapy, 2022

Applying antibiotics to susceptible bacterial cultures generates a minor population of persisters... more Applying antibiotics to susceptible bacterial cultures generates a minor population of persisters that remain susceptible to antibiotics but can endure them for extended periods. Recent reports suggest that antibiotic persisters (APs) of mycobacteria experience oxidative stress and develop resistance upon treatment with lethal doses of ciprofloxacin or rifampicin.

Advanced Healthcare Materials, 2022

Tuberculosis (TB), including extrapulmonary TB, is responsible for more than one million deaths i... more Tuberculosis (TB), including extrapulmonary TB, is responsible for more than one million deaths in a year worldwide. Existing methods of mycobacteria detection have poor sensitivity, selectivity, and specificity, especially in human tissues. Herein, we present the synthesis of a cholic acid-derived fluorescent probe (P4) that can specifically bind and stain the mycobacterium species. We show that P4 probe specifically binds with mycobacterial lipids, trehalose monomycolate, and phosphatidylinositol mannoside 6. P4 probe detects mycobacteria in polymicrobial planktonic cultures and biofilms with high specificity, selectivity, and sensitivity. Moreover, it can detect a single mycobacterium in the presence of 10000 other bacilli. Unlike the probes that depend on active mycobacterial enzymes, the membrane-specific P4 probe can detect mycobacteria even in formalin-fixed paraffin-embedded (FFPE) mice and human tissue sections. Therefore, the ability of the P4 probe to detect mycobacteria in different biological milieu makes it a potential candidate for diagnostic and prognostic applications in clinical settings. This article is protected by copyright. All rights reserved.

The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-d... more The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis (GWAS) using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, for the first time, we identified a strong association between the mutations in the DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis (Msm) and Mtb. Results show that variant mutations abrogated the function of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. Notably, in an in vivo Guinea pig infection model, the MutY variant outcompeted the wild-type strain. Colle...

Nanoscale, 2021

We showed that hydrogel-mediated delivery of a combination of anti-tuberculosis drugs is more eff... more We showed that hydrogel-mediated delivery of a combination of anti-tuberculosis drugs is more effective than oral delivery against tuberculosis.

Delhi, the national capital of India, has experienced multiple SARS-CoV-2 outbreaks in 2020 and r... more Delhi, the national capital of India, has experienced multiple SARS-CoV-2 outbreaks in 2020 and reached a population seropositivity of over 50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant B.1.617.2 (Delta) replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and partial reduction of immunity elicited by prior infection (median estimates; ×1.5-fold, 20% reduction). Seropositivity of an employee and family cohort increased from 42% to 86% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.One-Sentence SummaryDelhi experienced an overwhelming surge of COVID-19 cases and fatalities peaking in May 2021 as the highly transmissible and immune evasiv...

Nature Communications, 2019

Journal of Bacteriology, 2019

Bacterial alternative sigma factors are mostly regulated by a partner-switching mechanism. Regula... more Bacterial alternative sigma factors are mostly regulated by a partner-switching mechanism. Regulation of the virulence associated alternative sigma factor, SigF, of Mycobacterium tuberculosis, has been an area of intrigue with more predicted regulators compared to other sigma factors in this organism. Rv1364c is one such predicted regulator, the mechanism of which is confounded by the presence of both anti-sigma and anti-sigma-antagonist functions in a single polypeptide. Using protein binding and phosphorylation assays, we demonstrate that the anti-sigma factor domain of Rv1364c mediates autophosphorylation of its antagonist domain and binds efficiently to SigF. Furthermore, we identified a direct role for the osmosensor serine/threonine kinase PknD in regulating the SigF-Rv1364c interaction, adding to the current understanding about intersection of these discrete signaling networks. Phosphorylation of SigF also showed functional implications in its DNA binding ability, which may h...

Extracytoplasmic Function σ factors that are stress inducible are often sequestered in an inactiv... more Extracytoplasmic Function σ factors that are stress inducible are often sequestered in an inactive complex with a membrane-associated anti-σ factor. M. tuberculosis membrane-associated anti-σ factors have a small stable RNA gene A-like degron for targeted proteolysis. Interaction between the unfoldase, ClpX, and the substrate with an accessible degron initiates energy-dependent proteolysis. Four anti-σ factors with a mutation in the degron provided a set of natural substrates to evaluate the influence of the degron on degradation strength in ClpX-substrate processivity. We note that a point mutation in the degron (XXX-Ala-Ala) leads to an order of magnitude difference in the dwell time of the substrate on ClpX. Differences in ClpX/anti-σ; interactions were correlated with change in unfoldase activity. GFP chimeras or polypeptides of identical length with the anti-σ degron also demonstrate degron-dependent variation in ClpX activity. We show that degron-dependent ClpX activity leads ...

IUBMB life, Jan 22, 2018

The emergence of increasingly drug-resistant Mycobacterium tuberculosis strains has become a cruc... more The emergence of increasingly drug-resistant Mycobacterium tuberculosis strains has become a crucial public health concern. In order to effectively treat tuberculosis, it is imperative to find newer drug targets, which are important for the in vivo bacterial survival and persistence. Phosphorylation based signaling cascades modulated by eukaryotic-like serine/threonine protein kinases and phosphatase in M. tuberculosis, transduce extracellular stimuli to a cellular response ensuing pathogen's growth, persistence and pathogenesis. Of the 11 STPKs that M. tuberculosis genome encodes, three kinases, namely PknA, PknB and PknG and the sole serine/threonine phosphatase PstP are crucial for the intracellular survival of the bacteria. PknA and PknB regulates cell growth, cell wall synthesis and morphological changes during bacterial cell division; while PknG modulates metabolic changes in response to stress and aids in bacterial survival during latency like conditions. PstP functions t...

Biomacromolecules, 2017

Current membrane targeting antimicrobials fail to target mycobacteria due to their hydrophobic me... more Current membrane targeting antimicrobials fail to target mycobacteria due to their hydrophobic membrane structure, ability to form drug-resistant biofilms, and their natural intracellular habitat within the confines of macrophages. In this work, we describe engineering of synthetic antimicrobial polymers (SAMPs) derived from biocompatible polyamides that can target drug-sensitive and drug-resistant mycobacteria with high selectivity. Structure-activity relationship studies revealed that reduced hydrophobicity of cationic pendants induces enhanced and selective permeabilization of mycobacterial membranes. The least hydrophobic SAMP (TAC1) was found to the most active with maximum specificity towards mycobacteria over E. coli, S. aureus, and other mammalian cells. Membrane perturbation studies, scanning electron microscopy, and colony PCR confirmed the ability of TAC1 to induce membrane lysis and to bind to the genomic material of mycobacteria, thereby inducing mycobacterial cell death. TAC1 was most effective in perfusing and disrupting the mycobacterial biofilms; and was also able to kill the intracellular mycobacteria effectively without inducing any toxicity to mammalian cells. Cellular uptake studies revealed clathrin independent uptake of TAC1, thereby allowing it to escape hydrolytic lysosomal degradation and effectively kill the intracellular bacteria. Therefore, this manuscript presents the design and selective anti-mycobacterial nature of polyamide polymers with charged hydrophobic pendants that have ability to disrupt the biofilms and kill intracellular mycobacteria.

Asian Journal of Pharmaceutical and Clinical Research, 2017

Objectives: The purpose of the study is to characterize antimycobacterial phytoconstituent from... more Objectives: The purpose of the study is to characterize antimycobacterial phytoconstituent from ethyl acetate extract of dried bulbs of Allium sativum Linn. (Alliaceae) and elucidating the probable mode of action of the bioactive molecule.Methods: Serial extraction, Mycobacterium tuberculosis assay by agar well diffusion method, minimal inhibitory concentration by microplate alamar blue assay, Fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography (LC)-electrospray ionization (ESI)-mass spectrometry (MS)/MS, cell leakage assay, scanning electron microscopy (SEM), inhibition property of linear alkylbenzene sulfonate (LAS) in the presence of rifampicin on M. tuberculosis were performed.Results: Ethyl acetate extract displayed significant inhibition properties against M. tuberculosis H37Ra (MTCC 300). Subsequently, the bioactivity-guided fractionation was employed to purify the phytochemical. Analysis of FT-IR, LC-MS (ESI), 1H, and13C...

Journal of Biological Chemistry, 2016

Mycobacterium tuberculosis is an adaptable intracellular pathogen, existing in both dormant as we... more Mycobacterium tuberculosis is an adaptable intracellular pathogen, existing in both dormant as well as active diseasecausing states. Here, we report systematic proteomic analyses of four strains, H37Ra, H37Rv, and clinical isolates BND and JAL, to determine the differences in protein expression patterns that contribute to their virulence and drug resistance. Resolution of lysates of the four strains by liquid chromatography, coupled to mass spectrometry analysis, identified a total of 2161 protein groups covering ϳ54% of the predicted M. tuberculosis proteome. Label-free quantification analysis of the data revealed 257 differentially expressed protein groups. The differentially expressed protein groups could be classified into seven K-means cluster bins, which broadly delineated strain-specific variations. Analysis of the data for possible mechanisms responsible for drug resistance phenotype of JAL suggested that it could be due to a combination of overexpression of proteins implicated in drug resistance and the other factors. Expression pattern analyses of transcription factors and their downstream targets demonstrated substantial differential modulation in JAL, suggesting a complex regulatory mechanism. Results showed distinct variations in the protein expression patterns of Esx and mce1 operon proteins in JAL and BND strains, respectively. Abrogating higher levels of ESAT6, an important Esx protein known to be critical for virulence, in the JAL strain diminished its virulence, although it had marginal impact on the other strains. Taken together, this study reveals that strain-specific variations in protein expression patterns have a meaningful impact on the biology of the pathogen.

Nature Communications, 2015

Mycobacteria are successful pathogens that modulate the host immune response through unclear mech... more Mycobacteria are successful pathogens that modulate the host immune response through unclear mechanisms. Here we show that Rv1988, a secreted mycobacterial protein, is a functional methyltransferase that localizes to the host nucleus and interacts with chromatin. Rv1988 methylates histone H3 at H3R42 and represses the genes involved in the first line of defence against mycobacteria. H3R42me 2 , a non-tail histone modification, is present at the entry and exit point of DNA in the nucleosome and not within the regulatory sites in the N-terminal tail. Rv1988 deletion in Mycobacterium tuberculosis reduces bacterial survival in the host, and experimental expression of M. tuberculosis Rv1988 in non-pathogenic Mycobacterium smegmatis negatively affects the health of infected mice. Thus, Rv1988 is an important mycobacterial virulence factor, which uses a non-canonical epigenetic mechanism to control host cell transcription.

PLOS Pathogens, 2015

M. tuberculosis N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU Mtb) is a bifunctional e... more M. tuberculosis N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU Mtb) is a bifunctional enzyme engaged in the synthesis of two metabolic intermediates N-acetylglucosamine-1-phosphate (GlcNAc-1-P) and UDP-GlcNAc, catalyzed by the C-and N-terminal domains respectively. UDP-GlcNAc is a key metabolite essential for the synthesis of peptidoglycan, disaccharide linker, arabinogalactan and mycothiols. While glmU Mtb was predicted to be an essential gene, till date the role of GlmU Mtb in modulating the in vitro growth of Mtb or its role in survival of pathogen ex vivo / in vivo have not been deciphered. Here we present the results of a comprehensive study dissecting the role of GlmU Mtb in arbitrating the survival of the pathogen both in vitro and in vivo. We find that absence of GlmU Mtb leads to extensive perturbation of bacterial morphology and substantial reduction in cell wall thickness under normoxic as well as hypoxic conditions. Complementation studies show that the acetyl-and uridyl-transferase activities of GlmU Mtb are independently essential for bacterial survival in vitro, and GlmU Mtb is also found to be essential for mycobacterial survival in THP-1 cells as well as in guinea pigs. Depletion of GlmU Mtb from infected murine lungs, four weeks post infection, led to significant reduction in the bacillary load. The administration of Oxa33, a novel oxazolidine derivative that specifically inhibits GlmU Mtb , to infected mice resulted in significant decrease in the bacillary load. Thus our study establishes GlmU Mtb as a strong candidate for intervention measures against established tuberculosis infections.

Current Topics in Medicinal Chemistry, 2015

The highly persistent nature of Mycobacterium tuberculosis can be attributed to its lipophilic ce... more The highly persistent nature of Mycobacterium tuberculosis can be attributed to its lipophilic cell wall which acts as a major barrier in the process of drug discovery against tuberculosis. Glutamine synthetase plays a major role in nitrogen metabolism and cell wall biosynthesis of pathogenic mycobacteria. The current review focuses on the structural and functional aspects of Mtb glutamine synthetase and an overview of its reported inhibitors till date. Also in the present study, we employed a computational structure based drug design protocol for identifying novel inhibitors against Mtb glutamine synthetase (MtbGS). A total of 12 hits were identified based on e-pharmacophore related search and virtual screening, which were further tested for their in vitro MtbGS inhibitory activity. Three compounds (compound 6, 1 and 12) were found with IC50 less than 5 &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#181;M, of which compound 6 being top active with IC50 of 2.124 &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#181;M. Differential scanning fluorimetry studies were employed so as to measure the thermal stability of the protein complexed with the most active compound. Also the protein complexes with top three active compounds were subjected for molecular dynamics simulations to study their binding pattern and stabilization effect. The solvation free energies were also determined for these compounds, undertaking free energy perturbation studies, which can be used further for lead optimization in the process of anti-tubercular drug discovery targeting Mtb glutamine synthetase.

Journal of molecular modeling, 2015

Persistent nature of Mycobacterium tuberculosis is one of the major factors which make the drug d... more Persistent nature of Mycobacterium tuberculosis is one of the major factors which make the drug development process monotonous against this organism. The highly lipophilic cell wall, which constituting outer mycolic acid and inner peptidoglycan layers, acts as a barrier for the drugs to enter the bacteria. The rigidity of the cell wall is imparted by the peptidoglycan layer, which is covalently linked to mycolic acid by arabinogalactan. Uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) serves as the starting material in the biosynthesis of this peptidoglycan layers. This UDP-GlcNAc is synthesized by N-acetylglucosamine-1-phosphate uridyltransferase (GlmU(Mtb)), a bi-functional enzyme with two functional sites, acetyltransferase site and uridyltransferase site. Here, we report design and screening of nine inhibitors against UTP and NAcGlc-1-P of uridyltransferase active site of glmU(Mtb). Compound 4 was showing good inhibition and was selected for further analysis. The isothermal ...

Journal of Biological Chemistry, 2015

Background: Protein kinase A has been shown to be involved in modulating critical functions. Resu... more Background: Protein kinase A has been shown to be involved in modulating critical functions. Results: Although the activity of PknA is crucial for cell growth, the extracellular domain is expendable. Conclusion: Although the activation of PknA is necessary for its function, this is independent of PknB. Significance: PknA plays an indispensable role and is required for both in vitro and in vivo growth.